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BundleSeg exploration viewer for filtering #1035
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Hello @frheault, Thank you for updating !
Comment last updated at 2024-10-17 17:25:26 UTC |
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #1035 +/- ##
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- Coverage 68.79% 67.98% -0.81%
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Files 432 433 +1
Lines 22455 22764 +309
Branches 3039 3063 +24
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+ Hits 15448 15477 +29
- Misses 5709 5986 +277
- Partials 1298 1301 +3
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@GuillaumeTh Testing BundleSeg on a random big tractogram with the new --exploration_mode option and then using the viewer would be great for a tumor case showcase. |
Quick description
Implemented a new BundleSeg slider feature for filtering
Improved code to limit RAM usage by processing FreeSurfer surfaces (FSS) in chunks, making it easier to handle larger datasets.
New Features:
This mode searches all bundles at a higher pruning threshold (12mm).
A second script then visualizes the results and can save outputs in the specified folder.
Allows customization of the pruning distance threshold for all bundles.
Default value is 0.0, but this parameter can be adjusted based on the user's requirements.
Performance Improvements:
Slight speed optimization, especially for large datasets. For example, processing a 2GB tractogram with 6M streamlines and 51 atlas bundles takes approximately 5 minutes on 4 processes.
RAM usage is now optimized, allowing for smoother handling of large subjects on machines with limited resources (e.g., 5 large subjects processed on 4 CPUs with 32GB RAM).
Note: Using more than 4 processes (e.g., 8 or 16) doesn't significantly improve speed in this scenario.
Title:
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Type of change
Check the relevant options.
Provide data, screenshots, command line to test (if relevant)
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Checklist